Shinobi Reincarnation
by DragonMaster Jurabi Ozowa
Summary: Fluttershy was living her normal life, tending her animals' needs, but then she was attacked by an earth pony who accused her of causing the destruction his dimension. After her friends managed to save her, Fluttershy learns from Twilight about Kekkei Reincarnations, ponies who are the reincarnations of Shinobi from another world. It turns out that Fluttershy is one of them.
1. Prologue: A Destroyed World

_**Jurabi: Hello every fanfic writer and reader. I'm DragonMaster Jurabi Ozowa. I'm going to make a whole new story here on fanfic. This is a MLP: FIM and Naruto crossover. It basically follows the idea of another story that an author, 'Emma Iveli', wrote called: D Reincarnation which is a good fanfic, you should check it out. So, it's about 'Naruto' characters who has Kekkei Genkai be reincarnated into ponies. Here's my story so please enjoy.**_

* * *

**Prologue: A Destroyed World**

A medium sized white earth pony stallion with long red mane, purple eyes that were in a rippled pattern and a purple circle as its cutie mark walked through a ruined city. No matter where he went, he would always see dead trees and destroyed buildings. The sky had no sun. It was blanketed with gray clouds, slowly moving over head. Bits of paper and garbage were blown around with a steady wind. There were large caverns that were filled with molten hot lava and black smoke.

The white earth pony sat on a cliff as he witnessed the destroyed world before him. The world that was once beautiful and peaceful is now all but destroyed.

"How did all of this happen…?" the white earth pony asked with a tone of both disbelief and sadness.

"Rodross!" a voice shouted.

The white earth pony named Rodross turned to a purple mare unicorn with black mane and a red eye as her cutie mark.

"Virtra…what's wrong?" Rodross asked the purple filly unicorn named Virtra.

"He's appeared again!" Virtra asked.

Rodross immediately stood up, "Again? This is the third time this week…Alright, let's hurry." Rodross said as he and Virtra rushed through the ruined city.

* * *

They both arrived at a large ravine filled with lava. Then suddenly and slowly, a gigantic stone made monster with a spiky tail rose from the lava.

"Gravures…back again, I see!" Rodross shouted.

The giant stone creature named Gravures shouted a deafening roar.

"I've had enough of you anyway…I'm going to finish this!" Rodross shouted, "Asura Path!" That was when four hooves sprouted out of Rodross' back. "Virtra, have your Kekkei Blood Reincarnation power ready."

"Got it." Virtra said.

Rodross turned back to Gravures and rushed towards it. With a full force, he punched the monster in the chin; however, the monster recovered and struck back with a fire ball attack. Rodross dodge the attack and attacked the Gravures' legs but the Gravures knew he was attacking its legs and it did a body slam on him. Rodross caught the Gravures before it smashed him but because of the sheer weight, he knew he could hold on for long and Rodross moved out of the way as he let go of the monster.

Gravures then shot a beam of fire at Rodross who managed to dodge. Rodross then aimed for Gracious' face and punched it in the eye, but the Gravures retaliated by tail whipping Rodross into a wall. Gravures then charged at Rodross while he was stuck to a wall but Rodross quickly jumped over the monster.

"Time to end this…" Rodross then went under Gravures' feet and put his hands into the air, "Almighty Push!" Then a strong force enveloped the area as Gravures was sent flying across the lava pit but it recovered. Rodross was still panting hard and he couldn't move. Gravures took this chance to charge at Rodross; however, Virtra stood between them and her eyes turned red. Gravures suddenly stopped in its tracks and it slowly backs away and then it disappears into the lava.

Virtra, knowing for sure that Gravures was gone, turned back to the panting Rodross.

"Thanks." Rodross said.

"Rodross…you should have known that using that attack comes at a cost. You had to wait for 5 whole seconds until you could move again and that was all Gravures needed to kill you." Virtra scolded.

"I know…but I just wanted to end this." Rodross said.

"Yeah…but at least we stopped Gravures for now." Virtra said.

"True…but it'll just rise up from the lava like nothing ever happened." Rodross said as he smashed a nearby rock in rage, "I mean…what's the point of all this? Every time Gravures comes, we fight him, our attacks don't hurt him, he gets away…rinse and repeat. This will never end!"

"Everything has to end at some point, Rodross. Just calm down, okay?" Virtra said.

Rodross only shook his head, "Then how…? How do we completely destroy Gravures then?"

Virtra only lowered her head as she didn't have an answer.

"Not by force, of course." a voice said.

Rodross and Virtra turned to a black unicorn colt with black hair, green eyes, and a white and black circle as his cutie mark.

"Who are you? And what are you talking about?" Rodross asked the unicorn colt.

The unicorn chuckled as he said, "My name is Nephilim, the answer to your question, or so to say, the one who can point you to the answer."

"About how to destroy Gravures?" Virtra asked.

"Correct. You see, just as a tomato plant comes from a tomato seed or a hawk comes from its egg, everything has an origin. If Gravures can't be destroyed by force, then we need to stop him from ever being born." the unicorn named Nephilim said.

"So that's the way…So tell me, do you know how we can do that?" Rodross asked.

"Yes…but you'll need to follow me." Nephilim said as he walked away with Rodross and Virtra following.

* * *

Nephilim led them into a secret lab filled with paper work and files. There was also a computer that had a lot of data of previous records of history.

"You two are the Reincarnations of two Shinobi, am I correct?" Nephilim asked the two.

Rodross and Virtra were shocked by his knowledge of such a thing.

"Yes." Virtra said, "Mine is a boy named Ranmaru."

"And mine is…"

"Nagato Uzumaki, am I correct?" Nephilim finished for Rodross.

Rodross was surprised, "How did you know?"

"Your eyes were a big give-away. The eyes of the Rinnegan…a very powerful set of eyes, like the Sharigan. Do you know about Nagato?"

"Yes, he was the leader of a group called the Akatsuki. His goal was to bring peace to his world. Even though his methods were harsh, I understand how he felt given what he went through as a child. He was defeated by a boy named Naruto Uzumaki." Rodross said.

"Naruto Uzumaki…the child of prophecy. It's a shame that he didn't get reincarnated. The filly or colt reincarnation would have been a great help, but it seems that you are the only one who can stop Gravures." Nephilim said.

"Just tell me how." Rodross said.

"In order to fix this present timeline, you need to change the timeline of another dimension." Nephilim said.

"Wait…what? There's another dimension?" Virtra asked.

"Yes, and something happened in that dimension's timeline to cause all this." Nephilim said.

"Wait one minute; we need to travel to another dimension's past to change our dimension's future? You do realize that we're planning on doing two impossible things." Rodross said.

"But with my help, it isn't impossible because I have a Kekkei Genkai that allows me to travel through time and dimensions at the same time." Nephilim explained.

"No way…so who are you a reincarnation of?" Rodross asked.

"It doesn't matter now. What does matter is this: In order to change our past, you must eliminate the individual from the other dimension who awaken Gravures." Nephilim said.

Rodross went into deep thought and then said, "So…all I need to do is eliminate that one pony and our world is saved."

Nephilim nodded, "Correct. But look at these records of the event. This was the time when Gravures was freed and unleashed onto our dimension." Nephilim activated the computer to open the files that showed the time line and pictures of the other dimension. Everything looked peaceful and beautiful there.

"And you have this mare to blame." Nephilim casted a dark spell on the floor. Then the dark magic started to transform into a yellow mare pegasus with pink hair and butterflies as her cutie mark.

"So she's the one. The one who brought Gravures into our world. I can't believe it. What's her name?" Rodross asked.

"Her name is Fluttershy. Make no mistake, she may seem harmless but she is definitely the one who caused all out misfortunes." Nephilim said, "I'm afraid that you'll have to have no heart and soul to kill her. Are you ready?"

"If it mean saving this world, then I'll have to live with the guilt…" Rodross said.

"I'll send us back in that dimension's time to the point where Fluttershy was alive." Nephilim then casts another spell on himself, Rodross, and Virtra that caused all three of them to disappear.

* * *

_**To Be Continued…**_

_**The Shinobi reincarnations will be a mixture of OCs and canon characters (as you already seen), it will be explained why certain characters were reincarnated as mares... don't worry…And I'm sure that some of you may know that this story seems familiar to a certain game we know. That's basically where this story is going but not exactly. And if you're confused on what's going on, don't worry. This is a prologue so it's not supposed to make a whole lot of sense. Well, I hope that you enjoyed this chapter. And no, Naruto's not reincarnated in this story because only Kekkei Genkai users can do that in this fanfic. Sorry. So I hope you enjoyed this first chapter. If you have any suggestions, lay them on me.**_


	2. Fluttershy's Bad Day

**Fluttershy's Bad Day**

Rodross jumped out of the portal Nephilim created and viewed his surroundings. He wasn't in the same destroyed world he was in. This world was beautiful and lush with green grass and blooming flowers. The birds her chirping happily in the air that was fresh as it blew across the plain.

Rodross looked around to see that Virtra wasn't with him.

"Virtra? Virtra!" Rodross shouted but there was no answer.

* * *

Virtra appeared to have been sent to a shore with the pretty blue ocean and harsh sand. She walked around and checked her surroundings and saw that Rodross wasn't with her.

"So…this is the other dimension's past." She said, "I hope Rodross is okay. He can be insecure when he's alone." Virtra then started exploring the new world she's on.

* * *

"This is so unbelievable…" Rodross said in awe as he looked around the beautiful world. "So this is what I'm fighting for…" Rodross then got serious, "Now to fight for the future." He then started to walk along the path.

* * *

In Equestria, at the edge of the Everfree Forest, stood a small cottage. And living in that small cottage is none other than Fluttershy. Fluttershy is a very kind pegasus who is the animal care taker of Ponyville. She takes care of the animals that are hurt, sick, or injured. She is also shy so she doesn't like to be in very big crowds. Instead she likes to be in small groups of ponies like her friends. Her friends are Twilight Sparkle the alicorn who was originally a unicorn, her assistant Spike who was a baby dragon, Pinkie Pie an earth pony who likes parties, Applejack another earth pony who is a apple farmer, Rarity a unicorn who is a fashion designer, and her best friend, since foal hood, Rainbow Dash who the fastest Pegasus around.

Fluttershy began to go feed her animals for the day. She went to her kitchen and opened up her cabinets, but when she opened them she found out that she ran out of food. She looked at all of her cabinets, but none of them have food in them.

"Oh my." she said in surprise. "I'm out of food for the animals including myself. I need to go to the market place to restock."

So she went up to her bedroom and got her saddlebags with some bits to pay for the food she needs for herself and for her animal friends. Then she walked downstairs. She found her pet bunny, Angel, sleeping on the couch.

_"Angel seems tired."_ she thought. _"It'll be rude to wake him up. I'll get him a carrot for him while I'm there."_ And with that she exited her home and she headed for the market.

* * *

She made it to Ponyville's market place only to find a shock. Fluttershy was surprise to find that the market place is bustling with ponies here and there.

"Oh my." She said as she watched many earth ponies, unicorns, and pegasus walking about getting their needs at each stand. "This gonna be more difficult then I thought." She just sighed and she looked at her list of supplies that she needs to buy. After Fluttershy looked over her list, she proceeded to go to the stands that have the supplies that she needed to buy.

She started to walk over to the first stand that she needed to go which was a banana stand run by Banana Bliss. She came to the stand and greeted Banana Bliss.

"Hello Bliss." she greeted kindly.

"Hi Fluttershy." Bliss greeted back excitedly. "Do you know business is so crazy around here that it's bananas?" Bliss laughed at her own joke. "So what you doing on this very busy day?"

"Um…well." she nervously started. "I'm buying some supplies for me and my animals because I'm all out of food for the animals and me. Is it ok if I could buy some of your bananas?"

"Well of course you can. That will be 2 bits per banana." she replied kindly.

Fluttershy was about to take out her bits when suddenly something came speeding towards them and crash into the banana stand. It was none other than the Cutie Mark Crusaders.

"Ouch! Nice driving Applebloom." Scootaloo said sarcastically.

"Ah'm sorry Scoots. It's my first time riding this scooter of yours." replied Applebloom as she picked herself up.

"Well it's not my fault that you failed to listen what I told you about riding a scooter."

"Ah said ah was sorry."

The two crusaders continue to argue with each other, when Sweetie Belle spoke out. "Um, I hate to interrupt, you two, but we not only we scared Fluttershy but we crash into a stand."

This finally caught Scootaloo and Applebloom's attention and they turned their heads to the crushed banana stand.

"Oh my gosh, we're sorry Bliss that we wreck your stand." apologize Applebloom.

"Yeah I was trying to teach Applebloom how to ride my scooter." Scootaloo added.

"Also we're sorry, Fluttershy, for surprising you." Sweetie Belle also apologized.

"Well it's alright girls." Fluttershy responded. "I'm sure you three didn't mean it. What matters is you three aren't hurt."

"Yeah I'm sure you three fillies didn't mean it." Banana Bliss said. "Besides, this stand is very old anyways. Although, I'm sorry Fluttershy, but these three fillies squished all of my bananas during the crash."

"Oh that's ok I guess. Besides I hope nothing else bad happens while I'm buying food for me and the animals."

"Yeah today is just going bananas around the market, heh heh heh." Banana Bliss laughed at her own jokes again.

"Well, um…thanks Bliss I must go now. Take care you three." said Fluttershy kindly.

"Ok, Fluttershy. We're sorry again for this mess." Sweetie Belle apologized.

"Oh it's alright girls accidents can happen. Anyways bye girls bye Bliss." waved Fluttershy.

"Bye Fluttershy."

"Yeah bye Fluttershy."

"See you later, Fluttershy."

"Take care Fluttershy." waved back the CMC and Banana Bliss. And with that Fluttershy walked away to another stand leaving one pegasus, three fillies, and a smashed up stand.

"Well are you three gonna help me clean up this mess?" questioned Bliss.

"You're not gonna tell on us are you?" Applebloom asked.

"Well as long as you help me clean up this mess, I won't tell on you. As long as you three don't, 'tee hee', slip up." Banana Bliss responded and giggled at her 'funny' banana jokes. The three crusaders just shrug.

* * *

Meanwhile, Fluttershy was walking over to another stand. Since Banana Bliss' banana stand was crashed do to an accident, she has no bananas.

She sighed. _"I hope nothing else bad happens today."_ she thought to herself.

She walked over to a cabbage stand owned by an earth pony stallion. The stallion had a light green coat with a darker green mane and tail and he has a cabbage for a cutie mark.

"Hay there little missy." the stallion greeted nicely. "What can I do for you?"

"Well um I would like to buy your cabbages for my animals if you don't mind." she replied kindly.

"Well of course you can little missy." the cabbage seller responded. "Anything for your animals. That will be three bits please."

So Fluttershy took out three bits from her saddlebags and handed the cabbage salespony the bits. "Thank you very much little missy. Now hold on while I'll get the bags for you." So the salespony started to look for the bags.

* * *

Rodross had arrived at the market to see Fluttershy waiting for her cabbages.

"I finally found her…Fluttershy." Rodross then started to run towards her to do what he needed to do, a pink pony mare with a pink puffy mane and three balloons as her cutie mark stood in front of him.

* * *

The cabbage salespony returned with the cabbages Fluttershy ordered, "Here you go, little missy."

"Thank you very much." Fluttershy said as she left to find other shops.

* * *

"Oh…my…GOSH! WHO ARE YOU?! Are you new here?! I'm Pinkie Pie, the funniest most fun pony in Ponyville!" the pink pony named Pinkie Pie shouted as she started breathing heavily. "Did I ever mention you have weird eyes?"

Rodross backed away a bit, _"What's with this pony?"_ He thought, "I…um…" Rodross then noticed that Fluttershy wasn't where she was before. "Wha…? Where did she go?!" Rodross shouted searching for Fluttershy, "She must have run off…"

"Wait, did you miss somepony because of me?" Pinkie asked.

"Well...no…it's nothing. I'm sure she's still around here." Rodross said.

"I'm so sorry. But why don't I make it up to you with a party?!" Pinkie offered as she always does.

"No thanks…I'm a bit busy." Rodross said as he tried to leave but Pinkie caught up with him.

"Oh! Why don't I help you find this pony you're looking for?" Pinkie suggested.

"I'm sorry but I don't want to drag you into this. It's...very personal."

"Please…?"

"For the last time, no. I don't want to drag any other pony into this." Rodross said.

"It's either that or a party!" Pinkie shouted, "I owe you one so I'm helping you either way!"

Rodross sighed and said, "Okay…you can help me find this pony, BUT, when I find that pony, you get as far away from the both of us as you can."

"Why?" Pinkie asked in confusion.

"Because things might get ugly…" Rodross said as he continued his search with Pinkie Pie hopping behind.

* * *

Fluttershy made her way to the apple stand run by one of her best friends, Applejack.

"Oh I hope nothing bad happens here at Applejack's stand." she thought to herself. She headed over to the stand, when she receives a shock. The line to the stand was long. "Oh my…" she said to herself and then she sighed.

She came to the line to the apple stand. "This line is so long." she said.

"You're telling me." the pony in front of her said which revealed to be Bon Bon. "I was waiting here for two hours now."

"Oh, hi Bon Bon." she greeted. "How is Lyra?"

"Oh, she's fine." she replied kindly. "Well, how is your day?"

"Oh Bon Bon, this day so far is horrible. Applebloom and her friends accidently crash into Banana Bliss' banana stand." She replied as she looked at the ground.

"Oh don't worry Fluttershy." Bon Bon said. "I'm sure nothing else bad should happen. Although I think this long line is one of those bad happenings."

"Oh my, you're right. Well at least it's something less destructive."

"Hey can I join this conversation?" The two ponies looked behind them to see Lovestruck coming to the line. "Hello, Fluttershy. Hello, Bon Bon." she greeted nicely to them.

"Hello Lovestruck." The two ponies greeted back.

"How are you doing today?" asked Fluttershy.

"I'm doing alright. Helping run the flower shop, making some preparations for next year's Heart's and Hooves festival, and running the love committee here in Ponyville with some of my colleagues and your friend's sister-in-law meeting here sometimes. Thanks for asking." Lovestruck responded.

And so the three ponies talk to each other in the line while they wait for their turn. It made Fluttershy feel better. Soon it was Bon Bon's turn in line to be some apple's from Applejack.

"I've got to go. Bye Fluttershy, bye Lovestruck." she said the two ponies.

"Bye Bon Bon." greeted back the two other ponies.

And with that Bon Bon bought her apples and then she left. Then it was Fluttershy's turn and she went to her best friend Applejack's stand.

"Hello Applejack." she greeted kindly to the cowmare.

"Hay there sugarcube." Greeted back Applejack. "How are you doing on this mighty fine day?"

"Oh well getting some supplies for me and my animals. It's been a very tiring day." And so she told Applejack what happened on her day so far.

"Well that's sounds very exhausting and bad and what did my little sister and her friends did again?" asked Applejack who was worried and slightly mad about her little sister.

"Oh she was learning how to ride Scootaloo's scooter and she kinda crash into Banana Bliss' stand. She didn't really mean it. It was an accident."

"Well Ah'm glad that she ain't hurt and all, but Ah'm gonna have to talk to her later and give her a punishment. Ah'll also talk to Sweetie Belle and Scootaloo's parents too."

"Oh you don't have to. I saw them helping Bliss clean up her stand."

"Well Ah guess Ah don't have to have Applebloom and her friends punish, but Ah still have to talk to them. Anyways what can I do for you?"

"Oh can I buy some of your apples?" she asked.

"Well sure thing sugarcube. These are my last apples for the day." she answered.

"Aw, really? There the last batch? "Lovestruck asked from behind.

"Sorry there Lovestruck, but these are my last apples for today. You just have to come back tomorrow." Applejack said.

"Aw but I needed the apples for the love committee. We're having a party tomorrow and I need these apples to make my apple cookies for the party."

"Well Ah'm sorry there. Ah really am, but you have to come back tomorrow for me to restock on apples." Lovestruck felt heart-struck that she couldn't get the apples for her cookies for tomorrow. Fluttershy couldn't stand to see her sad, so she decide to be kind.

"Um…Lovestruck uh you could have my apples if you want." she said to Lovestruck.

Lovestruck was surprise. "Oh, but Fluttershy what about you?"

"I won't mind. Besides it looks like you need them more than me."

Lovestruck was speechless. "Fluttershy…this…this was very lovely of you thank you!"

"You're very welcome Lovestruck." Fluttershy kindly said.

And with that Lovestruck left with the last apples for the day.

"That was mighty kind of you, Fluttershy." Applejack said very proud of her friend. "But do you know that I'm still out of apples for today."

"Oh it's fine at least it isn't something bad that happened. " she responded. "Well I gotta go Applejack. I need to buy more things for me and the animals. So take care of yourself okay."

"Okay take care of yourself, sugarcube." And with that she left the apple stand just as Applejack cleaned up her stand for the day. "Ah hope else bad happens to her." she thought to herself.

* * *

And so Fluttershy's day at the market was good for now. Then her day got bad from some stand closing very early for the day to trying to calm an angry bear that smashed at the stand that she was at. But she manages to get half of the things on her list. She was mixed feelings for what the day has for her either it was a bad day or it was an ok day.

Fluttershy looked over her checklist to see what she needs to buy next. "Okay…let's see so far. I got the cabbages, the oranges, the pineapples, and the bird seeds. The rest…um…maybe tomorrow." She said to herself. "Now the last thing I need is." She looked at the last thing to buy on her list. "A carrot for Angel. Oh right." She looked around and found the carrot stand that is run by none other than Carrot Top aka Golden Harvest. "Oh good, there's no long line and there's plenty of carrots. Now I can get some lively carrots for Angel." So Fluttershy instead of walking do to her being exhausted of running around, she flew over there which she almost forgets that she is a pegasus.

* * *

Fluttershy went over to Carrot Top's stand. "Hi there Carrot Top." she greeted as usual.

"Hay there Fluttershy. How did you day go?" she asked.

"Well it's been…um…very exhausting. First Applebloom kinda crash into Banana Bliss' stand, then I gave the last apples to Lovestruck, and well I guess you can say the rest has been…um… well crazy." she replied feeling very exhausted.

"Well I say that is very exhausting."

"Yes and I only got half of the things I have on the list and the only thing I needed is some carrots for my pet Angel Bunny."

"Well let's hope nothing bad happens here. Anyway that will be five bits, but since you have a crazy day today I'll drop it down to two bits."

"Oh you don't have to."

"No it's fine I insist."

"Well thank you, Carrot Top." So Fluttershy opened her saddlebags and took out the two bits. She was about to hand Carrot Top the two bits, when suddenly a brown object landed on the carrots. The two ponies were surprise.

"What is that." questioned Fluttershy.

"A muffin…?" answered Carrot Top. "They're usually Derpy's favorite fo-" she stops what she was saying. She had a shocked face on her. She realized what this could mean.

"Um…Carrot Top what's wro-"

"Look out Fluttershy." She pushes Fluttershy out of the way just as a gray blur came rushing towards the carrot stand and smashed it into pieces. There left on where the stand used to be stood.

"Derpy!" Carrot Top shouted sternly.

"Oops sorry, Carrot Top." apologized Derpy Hooves.

Carrot Top sighed and said, "Sorry, Fluttershy, I guess no carrots for today." she sadly told Fluttershy.

"Oh well…" Fluttershy sighed, "It's alright. I guess that's enough shopping for today. See you later Carrot Top. See you later Derpy." she said sadly and so she walked sadly away leaving a smashed up carrot stand and two ponies to clean up the mess.

* * *

In Canterlot, Princess Twilight Sparkle had just finished her meeting with Princess Celestia. She was about to leave until she met her brother, Shining Armor.

"Going out, Twi?" Shining Armor asked.

"Yeah, big bro. I'm supposed to see my friends tonight. Pinkie's setting up my first anniversary of becoming an alicorn." Twilight said.

Shining Armor chuckled, "That sounds like her alright."

"Hey, maybe you and Cadence can come too." Twilight suggested.

But Shining Armor clobbed her lightly on the forehead, "Sorry, Twi, maybe next time."

Those words were all too familiar to Twilight, "Come on. Just because you're his incarnation doesn't mean you have to do the same things he did to his little brother."

"I know, but for some reason, I like it. And you can say it's a force of habit we both share." Shining Armor said.

"Right…" Twilight muttered, "I'll be seeing you soon, BBBFF." And then Twilight flew away from Canterlot to Ponyville.

* * *

Meanwhile, Pinkie Pie took Rodross to the bakery shop where she works at.

"Man…looking for one pony can be so tiresome. Would you like to rest, Rodross?" Pinkie asked.

"No thanks, I really need to look for this one pony." Rodross said.

"Oh come on! You're going to end up sleepy if you don't get any rest, plus it's late now. There's no point in looking for some pony if every pony is asleep." Pinkie said.

Rodross thought about it for a while, "I guess I could spend a night…"

"Yaay!" Pinkie then took out a sleeping bag, "I've got a sleeping buddy! Let's party!"

"No Pinkie! I'm just sleeping, nothing more." Rodross said much to Pinkie's displeasure.

"Okay…can I at least fire off the party cannon?" Pinkie asked with glee.

Rodross sighed, "Alright…but only once."

Pinkie shouted in joy as she bounced inside the bakery. Before Rodross could follow Pinkie Pie, something caught his eye, _"It's her…"_ He thought.

* * *

Fluttershy was walking home sadly. She didn't get much food for herself and the animals including something for Angel. She was depressed. But suddenly, she was knocked away by a kick in the pack. Fluttershy winced in pain as she saw who attacked her which was Rodross.

"I've been looking for you." Rodross said coldly.

"M-Me…?" Fluttershy asked meekly.

"Yes, Fluttershy I presume?" Rodross asked.

"Y-Yes…But…why did you…?"

"Because your actions will soon condemn us all!" Rodross shouted.

Fluttershy was starting to become both scared and confused.

"But I…I…" She whispered.

"Now…for the sake of my world's future. I will destroy you!" Rodross shouted.

"_Oh no…Could this day get any worse…?"_ Fluttershy thought.

* * *

_**To Be Continued…**_

_**Jurabi: I hope that you enjoyed this chapter. Not many reviews but I'm sure more will come. I'm sure that you can guess who Twilight and Shining Armor are incarnations of.**_


	3. Reincarnations

_**Jurabi: Well, this story's off to a good start. At first, I though it wouldn't get many readers; however, it seems I was wrong. Might as well press on, but first I'll have to answer one random MLP question from my MLP question box. –digs into the box and takes out a random piece of paper- Alright…the question is: Who is your favorite MLP character out of the Mane Six? Well…between Rainbow Dash and Twilight, I'll have to choose Fluttershy since she's very similar to Hinata Hyuga from 'Naruto'. She's cute, kind-hearted, and loving; plus, she can be a strong girl if you piss her off. In honesty, that's my kind of female character. I'm not all that interested in 'Princess Peach type' females, if you know what I mean.**_

* * *

**Reincarnations**

Fluttershy stood in fear at the pony before her planning to destroy her. When she looked at Rodross' purple eyes, a memory suddenly kicked in. Three strange creatures in clothing. One of them was pinned to the ground while the other two were standing. Fluttershy could tell that one of them was the female standing in front of the male pinned on the ground, but the memory disappears.

Fluttershy looked back at Rodross' eyes, "Pain…?"

"Excuse me?" Rodross asked confused.

"You're…Pain..." Fluttershy said, "But…how's that possible?"

Rodross' eyes widened in realization as he thought, _"Pain…Right…Nagato's other name in the Akatsuki. But how does this mare know of him?"_ Rodross shook off the thought, "Asura Path!" He shouted as his four hooves sprouted from his back scaring Fluttershy, "This is for the future of my world." He then pointed his hoof at Fluttershy, "Deva Path."

Suddenly, Fluttershy was being pulled towards Rodross by a mysterious force. Fluttershy was so afraid about what was happening that she only covers her eyes. With full force, Rodross hoof punched her in the stomach with three of his hooves which sent her crashing across the ground. Clutching on her stomach, Fluttershy slowly stood back on her four hooves with small drops of blood coming from her mouth.

Fluttershy tried with all her might to stay up, but she eventually fell down again. She could only sit there like a statue as she witness Rodross create a clone of himself. Tears fell out of her eyes as Rodross had a confused look.

"Is this a joke? How can somepony like you destroy my world?" Rodross asked.

"Wh…What do you…mean…?" Fluttershy asked.

"It doesn't matter. For the sake of my world, you have to be destroyed." Rodross said as he pointed his hoof at her again, "Asura Attack." His hoof suddenly turned into a cannon that was preparing to fire. But then, Rodross sensed something coming and dodged a high speed kick that came out of nowhere.

Fluttershy slowly picked her head up to see a blue pegasus mare with a rainbow-colored mane and a cloud with a rainbow colored lightning bolt as her cutie mark.

"R-Rainbow Dash…" Fluttershy whispered.

Rainbow Dash looked back at her injured friend, "Fluttershy! Are you okay?"

"I…I…" Fluttershy's eyes closed shut as she lost consciousness.

Rainbow Dash sent Rodross a chilling glare, "Who do you think you are attacking Fluttershy like that?"

"You don't understand what I'm trying to do here." Rodross said, "Please move out of the way. I don't wish to hurt you."

"I may not know why you want to harm Fluttershy, but I won't stand by and let you continue." Rainbow Dash said as he flew up in the air and tried to tackle Rodross, but he easily dodges it. Rainbow Dash circles around and tries to kick Rodross, but he easily dodges again.

Infuriated, Rainbow Dash flew high up in the sky and put ever ounce of effort into her speed creating a Rainboom.

Rodross still dodge the attack, but Rainbow Dash's kick grazed his right foreleg. While landing, Rodross stumbled a bit but balanced out his landing.

"Now's my chance." Rainbow Dash thought as she flew to Fluttershy and picked her up.

Rodross notices this and points his hoof cannon, "No you don't. It's time to end this."

"STOP!" a voice shouted.

Pinkie Pie gets in between Rodross and Rainbow Dash.

"Pinkie Pie? Get out of the way! This is my mission!" Rodross shouted.

"No way! I'm not moving one bit!" Pinkie shouted.

"Thanks, Pinkie, we appreciate it." Rainbow Dash then flew away with Fluttershy in her arms.

After Rainbow Dash and Fluttershy were out of eyesight, Rodross was angry at a missed chance.

"Pony feathers, Pinkie. What's the big idea?" Rodross asked.

"I should be asking you the same thing, Rodross. You…were after Fluttershy? Were…Were you planning to kill her?" Pinkie asked in confusion.

Rodross' hoof cannon turned back to normal, "She's responsible for destroying my world."

"What?! That's crazy! Fluttershy would never do that!"

"But it's true! Fluttershy's actions here will cause the devastation of my dimension, so I must-"

"NO!" Pinkie shouted as tears fell down her eyes, "I don't care what you say, I don't believe it. No matter how true you think it is, Fluttershy will never destroy or hurt anything. What if what you were told was a lie?"

"Why are you defending that pony so much?"

"Because she's my friend. I'm sure you would defend your friend if he or she were accused of something like this."

Rodross' jaw dropped at Pinkie's statement. "You're right. I would have protected my friends if they were accused of something like this…but unlike you, I wouldn't let my feelings for them get in the way of straight facts."

"The same facts that could be lies?" Pinkie asked. "I don't buy it…If I want to choose between your make-believe story and Fluttershy, I would choose Fluttershy anytime, any day." Then Pinkie Pie rushed off leaving a shocked Rodross to ponder on her words.

* * *

Twilight had finally arrived at her library only to find a Spike searching for something.

"Hey, Spike. I'm back." Twilight greeted.

"Yeah, great to see you. Twilight, do you know where the bathroom is again?" Spike asked frantically.

Twilight sighed and said, "Down the hall, second door to the left."

"Thanks!" Spike shouted already half-way there.

"Geez…" Twilight muttered to herself, "It's only been a week since we had this new library. Why can't that dragon simply find the bathroom?" Twilight shook her head and looked at the clock, "Pinkie Pie's party won't be for another few hours…I wonder…" Twilight headed to one of the many book shelves she had in her library and searched for a specific book. "Okay…R…R…Re…Re…Ah! Here it is." Twilight used her magic to bring out a green book.

That was when Spike came out of the bathroom with a relieved smile, "Thank Celestia you came when you did, Twilight. I let out a huge waterfall in there."

"Seriously Spike? You still couldn't find the bathroom?" Twilight asked in disbelief.

"Cut me some slack, I checked every door in this library." Spike then sighed, "I miss the old one…"

Twilight then sent Spike a sympathetic smile, "I know, but sometimes, everypony has to move one no matter what they lose."

"So what are you planning on reading now?" Spike asked noticing the book Twilight pulled out.

"Oh this? It's a book called Reincarnations. It's when-" Twilight was suddenly interrupted by a forced door opening.

"Twilight, are you here?!" Rainbow Dash shouted.

Twilight teleported down stairs to meet Rainbow Dash only to be shocked beyond belief when she saw Fluttershy injured in her arms.

"Oh my gosh…Fluttershy!" Twilight shouted.

"What's the matter Twi-Whoa!" Spike shouted seeing Fluttershy as well.

"What happened to her?" Twilight asked.

"She was attacked by some pony." Rainbow Dash said.

"Alright, let's get her into bed." Twilight said as she and Rainbow Dash took Fluttershy to a nearby bed to rest. "Okay, Rainbow, you said a pony attacked her?"

"Yeah, I was just doing what I usually do: Chilling in the sky, until I saw Fluttershy being sent flying with blood coming out of her mouth. That was when I saw this colt pony and knew that he attacked her so I defended her." Rainbow Dash explained.

"What can you tell me about this colt?" Twilight asked.

"Well…there's nothing much to explain but I saw two of him."

"Two of the same exact pony? That doesn't seem right." Spike said.

"I could tell that those two weren't ordinary ponies. One of them had more than his four hooves; there were two extra ones on his back." Rainbow said. "I tried to hit the pony who hurt Fluttershy, but he kept dodging all of my attacks. He even dodged my high speed Rainboom kick."

"Wait…Rainbow Dash, what was the other pony doing while attacked the one you were talking about?" Twilight asked.

Rainbow Dash rubbed her head trying to remember, "Well…the other pony was just standing there; staring at us. I wasn't sure why."

Twilight's eyes widened as she asked, "One more question: Did anything about this pony seem strange to you?"

"Well…he did have these weird purple eyes." Rainbow Dash said.

Twilight's jaw dropped, "That's all I need…Rainbow Dash, go get Rarity and Applejack and bring them here."

"Sure thing, but why?"

"I'll explain later. Now go."

Without a word, Rainbow Dash flew off to find Rarity and Applejack. Twilight went to Fluttershy's bedside.

"Am I missing something, Twilight?" Spike asked.

"No…well…yes, you are. It's just…how can his incarnation be here?" Twilight asked.

"Okay, back up. First off, what in the world of Celestia is an incarnation?"

"An incarnation is when a strong spirit of a being is transported into the soul of another's. You see in Equestria, there are ponies that are the incarnations of special humans. You remember humans, don't you?"

"Yes, from that alternate world we visited, right?"

"Correct, now these humans are more special than the humans we met in that world. These humans call themselves Shinobi. They're…um…I'm not sure how I can explain it. Shinobi are…well…ninjas in a way. But these ninjas possess powerful abilities that clearly aren't magic. They call it: Catra…? No wait…Chakra. Now, most ponies are the incarnations of different types of Shinobi. I know that there are two types: Kekkei Genkai Reincarnates and Clan Reincarnates."

"So…what's the difference?"

"The difference is that Kekkei Genkai is a blood-type ability, while Clan abilities don't have to be a common trait. I hope I didn't confuse you, Spike."

"No…I think I've got it." Spike said, "Now then, you were asking how a reincarnates could be here?"

"Yes, well you see-" Twilight was cut off by the doors opening.

"I brought Applejack and Rarity, Twilight." Rainbow Dash said.

"Excellent. Rainbow Dash, Spike, can you leave us alone for a while?" Twilight requested.

"Sure, but…" Spike was stopped when Rainbow Dash put a hoof on his shoulder.

"Take all the time you need, we'll go look for Pinkie Pie." Rainbow Dash said as she picked up Spike and flew off.

"Alrighty, sugarcube," Apple Jack started, "What's all the commotion about?"

"You should see for yourself." Twilight said showing them Fluttershy.

"My goodness, what happened to her?" Rarity asked.

"She was attacked…by Pain's incarnation." Twilight said.

Apple Jack and Rarity's eyes widened and their jaws dropped from the shock.

"That's impossible, dear. It was reported by the Reincarnates Division that Pain's reincarnates colt was murdered 5 years ago." Rarity said.

"Nopony's ever caught the murderer ever since. It sure doesn't make sense." Applejack said.

"Yes, that's what's troubling me." Twilight said.

"Do you think we should contact Princess Celestia?" Rarity asked.

"No…not yet. Not until we can figure out what's going on. For all we know, this could be a wild goose chase. Besides, even when 5 years have passed, Celestia doesn't seem like the kind of pony who would simply forgive and forget what that colt's done."

"Whatcha mean by that?" Applejack asked.

"It's nothing you should worry about…"

"So…any idea on where to start?" Rarity asked.

"What we need to do first is meet an old friend of mine. He should point us in the right direction." Twilight said.

"What about Fluttershy? After what happened to her, we sure can't leave her like this." Applejack said.

"You're right…" that was when realization kicked in, "No wait, it's fine. Discord can help us with that issue."

"You called?" Discord's voice said as the God of Chaos appeared in a tuxedo, "Is there anything you need, Master Twilight?" A glass of water appeared in his hand, "A glass of water? A massage? A gown polish?"

"Uh…Discord. I appreciate your comedy, but this is a serious situation." Twilight said.

"Serious? Serious is my middle name. Next to 'Chocolate Rain Creator' and 'Chaos' and…"

Twilight facehoofed herself while Discord named off the dozens of middle names he conveniently has as she levitated Fluttershy's bed in front of Discord.

"…and 'God of Mischief'…Oh wait 'Chaos'. Mischief was already taken and- *gasps* My dear Fluttershy! What's happened to you?!" Discord's comedic attitude instantly changed to a real serious one when he saw Fluttershy's unconscious body.

"We need you to watch over her. I'm not sure about what's going on, but her attacker is still out there." Twilight said.

Discord did an army salute and dressed in army clothing, "Ma'am, yes ma'am." Discord stood at straight attention like a statue.

Twilight nodded as she, Rarity, and Applejack exited the library.

"I've never seen Discord act like that before." Rarity said.

"That's because he's protecting a friend, especially his first best friend." Twilight said.

"So, sugarcube, who's this pony feller you want to meet?" Applejack asked.

"I'll introduce her to you when we get there." Twilight said.

* * *

Rodross was away from Ponyville and was sitting next to a lake staring at his reflection still pondering on Pinkie Pie's words.

"There you are." a voice called out.

Rodross turned his head to see Virtra, "Hey…"

"I was wondering where you were. So any luck finding Fluttershy?" Virtra asked.

"Well…about that…" Rodross didn't want to explain how things went.

Virtra seeing his hesitation sat down next to him, "What's the matter? What went wrong?"

"I did find Fluttershy and…I was about to do what we came here to do but…two ponies got in the way. I didn't want to murder anyone else."

"I see…" Virtra said.

"Listen, I need your honest opinion."

"Yes?"

"To kill somepony to save the world…is that really the only option we have?"

Virtra sighed, "There you go again. Being naïve…My honest opinion…well…sometimes there are risks in life. Some of those risks are chances as well. Life well have most risks that we have to take if we're going to save our world. Can you take risks, Rodross."

Rodross stayed silent pondering on the question, "Well…I'm not willing to take a risk unless we know what the future will be like if we do or don't take action. We probably should learn more about Fluttershy before we do anything."

"So how do we do that?" Virtra asked.

"Do you remember the Everfree Forest back in our world?"

"Yes."

"They say that there is a powerful hermit who lives in those woods. I don't know much about him or her, but it is said that the hermit knows almost everything that happens in Equestria. We should probably go see this hermit and ask him or her about Fluttershy. Then we can judge whether we should eliminate her or not."

"Sounds like a plan."

"Then let's get going then." Rodross said as he and Virtra journey to the Everfree Forest.

* * *

Inside another dark forest, Nephilim was walking along the path until a voice called.

"Well, well, well, look what the cat dragged in." a mare voice called. Nephilim slowly turned to a black mare with a green mane and green eyes and a black star as her cutie mark.

"Naomi…what do you want?" Nephilim asked coldly.

"Aww…no hello or it's been a while? You're no fun." the mare named Naomi said. "So…it's the same plan as always?"

"Correct."

"Oh, so can I eliminate Fluttershy then? Please?" Naomi asked.

"No…" Nephilim said.

"But why?"

"Because I need her alive and strong. I've sent two strong ponies to try and eliminate her. Little do they know that they are the forces that will drive Fluttershy to train and become strong. That is the level I want her to be at for my plan." Nephilim said. "Do you understand?"

"Yes sir…" Naomi replied in a disappointed tone.

"Good…but I want you to do something with the mare but DON'T kill her." Nephilim said.

"Really? Of course, no killing, stabbing, or any other gruesome stuff. So what do you want me to do?" Naomi asked.

Nephilim gestured her to come closer and whispered into her ear. Naomi then leapt in joy, "Oh, I wanted to do that too."

"Remember, don't kill her. Only make her remember the pains of the past." Nephilim said.

"Yes, of course, that's what only I can do. It'll be great to see her pretty scared face again. I wonder if she'll remember me." Naomi said viciously as she walks along the path. "Better beware, Fluttershy…you're in for a scare."

* * *

_**To Be Continued…**_


End file.
